New peptide antibiotic stops bacteria by binding where no drug has before

New peptide antibiotic stops bacteria by binding where no drug has before

Lariocidin hits drug-resistant bacteria where others fail - by hijacking the ribosome to a new location, bypassing defenses and opening the door to a new generation of antibiotics.

Lariocidin, a lasso-shaped peptide with promising antibiotic properties. (Graphics: Dmitrii Travin and Yury Polikanov). Investigation: A broad lasso peptide antibiotic that targets the bacterial ribosome

Researchers at McMaster University, in collaboration with researchers at the University of Illinois at Chicago, have discovered a powerful candidate antibiotic that can kill a wide range of bacteria, including those resistant to existing antibiotics. They published the results in the journalNature.

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Antibiotic resistance occurs when bacteria evolve and develop resistance to existing antibiotics. It is a major public health crisis worldwide that makes the treatment of bacterial infections challenging. More than 4.5 million deaths occurred due to antibiotic resistance in 2019.

The World Health Organization (WHO) has identified gram-negative bacteria as a critical threat because of their ability to develop and spread antibiotic resistance, making it a top priority to discover new antibacterial drugs.

Various peptide-based antibiotics produced by microbes have shown high effectiveness in treating bacterial infections. Most of these antibiotics are produced outside the ribosome, the cellular structure responsible for protein synthesis, by specialized peptide synthetases encoded in the genomes of antibiotic-producing microbes.

Ribosomally synthesized and posttranslationally modified peptides are rapidly gaining popularity as a novel class of antibiotics. The post-translational modifications set the three-dimensional shape of these peptides, facilitate their interactions with target proteins, and protect them from degradation by cellular peptidases.

Lasso peptides are biologically active molecules with a distinct, structurally restricted nodal fold that belong to the class of ribosome-synthesized and post-translationally modified peptides. Lasso peptides act on multiple bacterial targets; However, none of them have been identified as targeting the bacterial ribosome.

In thisNatureThe article, Professor Gerry Wright of McMaster University and his team reported the identification of a new lasso peptide called lariocidin that functions as a broad-spectrum antibiotic by targeting the bacterial ribosome at a unique location.

Importantly, lariocidin not only inhibits protein synthesis by interfering with translocation, but also induces translation errors (miscoding), giving a dual mechanism of action.

The researchers note that lariocidin meets three important criteria for a next-generation antibiotic: a novel structure, a new binding site and a distinct mechanism of action.

Lasso-shaped antibiotics involved in UIC evasion drug resistancePlay

The study

The researchers created a collection of environmental bacterial strains by culturing them in the laboratory for about a year. Such long-term culture enabled the growth of the slowest-growing bacteria that would otherwise be overlooked.

They produced methanolic extracts of individual bacterial colonies and tested them against a multi-resistant bacterium. This led to the identification of a novel lasso peptide, lariocidin, produced by a type of soil bacterium calledPaenibacillus.

By conducting a series of biochemical and structural experiments, they found that lariocidin can kill a wide range of bacteria, including multidrug-resistant strains, by inhibiting ribosomal protein synthesis.

They also found that lariocidin binds to a unique site in the small ribosomal subunit of bacteria that is significantly different from the sites of action of existing antibiotics that target the small ribosomal subunit. This unique binding site allowed lariocidin to bypass the defense mechanisms that bacteria have evolved to resist other drugs.

This ribosomal binding mode relies primarily on interactions with the RNA backbone rather than the nucleobases, making it less susceptible to resistance caused by mutations in the binding site.

In laboratory-adapted bacterial strains with a single ribosomal RNA operon, the researchers identified rare spontaneous mutations in the 16S rRNA that reduced laricin susceptibility.

The team highlighted that developing antibiotics that act at previously unused ribosomal sites offers a way to circumvent common resistance mechanisms.

As observed by researchers, lariocidin's unique structure allowed it to overcome the challenges other antibiotics typically face in targeting the bacterial ribosome. Mechanistically, antibiotics first enter the bacterial cell through transporters to inhibit protein synthesis, particularly the ribosome. However, bacteria can modify or remove these transporters to block entry of antibiotics.

In contrast, the strong positive charge of lariocidin allowed the bacterial cell to enter directly through the membrane without the need for transporters. This specific feature made lariocidin a broad-spectrum antibiotic.

Because lariocidin bypasses the need for specific transporters, it can enter a wide range of bacterial species, reducing the likelihood of resistance developing through transporter mechanisms.

Using a mouse model fromAcinetobacter baumanniiIn infection, researchers showed that lariocidin can significantly reduce bacterial loads in various organs. They further found that the peptide has a low propensity to generate spontaneous resistance and has no cytotoxic effects on human cells.

Antimicrobial activity was even stronger in nutrient-limited media mimicking host environments, indicating improved clinical potential compared to standard susceptibility testing in rich media.

This enhanced potency was associated in part with the presence of bicarbonate, which increases the bacterial membrane potential and promotes uptake of the positively charged lariozidine.

All of these features made lariocidin a promising candidate for further development into a clinical antibiotic for the treatment of serious multire-resistant bacterial infections.

The study also identified a structurally related isoform lariocidin B (Lar-B), which contains an additional isopeptide bond forming a double lariat structure. This may improve the stability of the molecule and marks Lar-B as the founder of a proposed new class (Class V) of lasso peptides.

By conducting bioinformatics analysis of available bacterial genomes, the researchers suggested that there may be other ribosome-targeting lasso peptides that have yet to be discovered in nature.

They identified dozens of lariocidin-like biosynthetic gene clusters (BGCs) across multiple bacterial phyla, including Actinomycetota, Bacilliota and Proteobacteria, indicating a broad evolutionary distribution of this antibiotic scaffold.

The researchers describe lariocidin as the first member of a previously unrecognized family of ribosome-targeting lasso peptides, with the potential for even more potent analogues to be discovered.

The researchers are now working to develop strategies to modify the Lasso peptide and produce it in large quantities for clinical development.

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